About us and our services CMSI

​Chalmers Mass Spectrometry Infrastructure, CMSI, is a Chalmers infrastructure that provides access to mass spectrometry analyses to researchers both within and outside Chalmers.


Metabolomics services at CMSI include both standard untargeted profiling using both UHPLC-QTOF and GC-MS instruments. In addition, we offer a combined untargeted and targeted metabolomics method that both collects untargeted scanning data as well as targeted data on a set of metabolites, including potential biomarkers of food intake (see reference below). In general, untargeted metabolomics is used for biomarker discovery and, thus, results are expressed in relative responses rather than in absolute concentrations. For identification metabolites, we use both in-house and commercial libraries and continuously work to improve our libraries, but due to the nature of the analysis, the majority of potential metabolites still remain unknown. For work focusing on mechanisms rather than biomarker discovery, using GC-MS or GC-MS/MS may be a good alternative, as many metabolites centred around known biochemical pathways are detected and identified.Instrument used for this service: Agilent QTOF 6550 with Infinity II UHPLC and Shimadzu TQ8030 GC-MS/MS.


Lipidomics services at CMSI include both lipid class separation and quantification using HPLC-CAD and lipidomics profiling using a UHPLC-QTOF system. Lipidomics profiling offers the detection of an array of different lipids with relative quantification by using class specific internal standards and calibration curves for the different lipid classes. Thus, the reported data is semi-quantitative. Chalmers is part of the national BioMS VR-infrastructure, and can provide analyses supported by this infrastructure.

Instrument used for this service: Agilent QTOF 6520 with Infinity UHPLC.

Fatty acids

Fatty acid analysis is one of the standard analyses at CMSI. Samples are analysed either by using a GC-MS or a GC-FID, depending on the purpose and required throughput of the analysis.

Instrument used for this service: Thermo GC-MS or GC-FID.

Organic acids

Organic acid and sugar analysis in fermentation samples

Standard measurement of organic acids and sugars for yeast fermentation control purposes.

Instrument used for this service: Dionex HPLC-UV-RI.


Alkylresorcinols are biomarkers of whole grain intake. The CMSI offers a quantitative, high throughput method for measuring the standard, odd-chained, alkylresocinols including C17, C19, C21, C23 and C25, as well as the recently discovered even-chained homologues C18, C20, C22 and C24. Alkylresorcinols in food can also be analysed using either HPLC-FLD or GC-MS for difficult matrices.

Instrument used for this service: Sciex QTRAP 6500+ with Exion UHPLC.

Amino acids

Amino acid analysis includes both free and total amino acids. The service is quantitative and includes both essential amino acids and amino acid related molecules. The method is able to separate 1- and 3-methylhistidine and leucine, isoleucine as well as allo-isoleucine (requested separately) from each other

Instrument used for this service: Sciex QTRAP 6500+ with Exion UHPLC.


There are currently two mass determination services offered at CMSI:

  1. Low-resolution mass spectrometry (LRMS)
  2. High-resolution mass spectrometry (HRMS)

The LRMS service is primarily designed for synthetic chemists and for other researchers who want to find out the mass of products or intermediates for providing information on their reaction or purity of their isolated molecule. Available ion sources: electrospray (ESI) and atmospheric chemical ionization (APCI). The normal service includes training on the LC-MS instrument and providing analytical support for the user to run their own samples.

The HRMS service is primarily designed for analysis of pure samples to acquire accurate mass. Available ion sources: electrospray (ESI) and atmospheric chemical ionization (APCI). The normal service includes running the samples without a column. You will get a brief report with the detected accurate mass, the ppm error, and a mass spectrum chromatogram of the detected compound.

Instrument used for this service: Agilent 6120 SQ MS and Agilent 6520 QTOF.

Method development

CMSI is always open for method development projects and, in addition to being great fun, this is one of the core competences of our infrastructure. CMSI is specialized in measurement of small molecules using different hyphenated mass spectroscopic techniques and has an impressive collection of instruments for this purpose. Thus, by collaborating with CMSI in method development users get access to both well maintained, high-end instruments and to the knowledge inbuild into the infrastructure

Interested? Just send an email to cmsi@chalmers.se with a description on what you want to measure!